United Arab Emirates University Scholarworks@UAEU Biology Theses Biology 4-2018 Metagenomic Profile of the Bacterial Communities Associated With Ornithodoros Muesebecki (Acari: Argasidae) Ticks On Socotra Cormorant Colony in the United Arab Emirates and Presence of Three Important Pathogenic Groups in Them Raheel Nasser Alkayyoomi Follow this and additional works at: https://scholarworks.uaeu.ac.ae/bio_theses Part of the Environmental Sciences Commons Recommended Citation Alkayyoomi, Raheel Nasser, "Metagenomic Profile of the Bacterial Communities Associated With Ornithodoros Muesebecki (Acari: Argasidae) Ticks On Socotra Cormorant Colony in the United Arab Emirates and Presence of Three Important Pathogenic Groups in Them" (2018). Biology Theses. 5. https://scholarworks.uaeu.ac.ae/bio_theses/5 This Thesis is brought to you for free and open access by the Biology at Scholarworks@UAEU. 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If ! )) o:ui.a.JpU IG...u I u I La!JI Ci5t.o b UJ\EU '\J United AT�b EmiTat�s U�iveTsity United Arab Emirates University College of Science Depaliment of Biology METAGENOMIC PROFILE OF THE BACTERIAL COMMUNITIES ASSOCIATED WITH ORNITHODOROS MUESEBECKI(ACARI: ARGASIDAE) TICKS ON SOCOTRA CORMORANT COLONY IN THE UNITED ARAB EMIRATES AND PRESENCE OF THREE IMPORTANT PATHOGENIC GROUPS IN THEM Raheel asser Mohammed Hmoud Alkayyoomi This thesis is submitted in partial fulfilment of the requirements fo r the degree of faster of Science in Environmental Sciences Under the Supervision of Dr. Mohammad Ali AI-Deeb April 20 18 II Declaration of Original Work I, Raheel asser Mohammed Hmoud Alkayyoomi , the undersigned, a graduate student at the United Arab Emirates Uni ersity (UAEU), and the author of this thesis entitled "Aletagellomic Profile of the Bacterial Commlll7itie As odated with Ol71i1hodoro AIlIe ebecki (Acari: Arga ;dae) Tick 017 ocotra Cormorant Colony ;'7 the United Arab Emirate and Pre ellce of Thre important Pathogenic Groups in Them", hereby, solemnly declare that this thesis is the original research work that has been done and prepared by me under the super ision of Dr. Mohammad Ali Al­ Deeb, in the College of cience at UAEU. This work has not previously been presented or published or fo rmed the basis fo r the award of any academic degree, diploma or a similar title at this or any other university. Any materials borrowed from other sources (whether published or unpublished) and relied upon or included in my thesis have been properly cited and acknowledged in accordance with appropriate academic conventions. I furtherdec lare that there is no potential conflict of interest with respect to the research, data collection, authorship, presentation and/or publication of this thesis. -��=--�-.l-.-=-"�"""'------ - Student's Signature Date :z,o - S- 2--7)I <t 1lI Copyright© 2018 Raheel Nasser Mohammed Hmoud Alkayyoomi All Rights Reserved IV Advisory Committee I) dvisor: Mohammad Ii AI-Deeb Title: Associate Professor Department of Biology College of cience 2) Co-advisor: abir Bin Muzaffar Title: Associate Professor Department of Bio logy College of cience V Approval of the Master Thesis This Master Thesis is approved by the following Examining Committee Members: 1) Advisor (Committee Chair): Mohammad Ali AI-Deeb Title: Associate Professor Department of Biology CollegcofScience ~ ~ Signature ----~-\---'"----=--~----r'-:;......--.-- Date J- 5 - '2 ° 18 2) Member: Sofyan Alyan Title: Associate Professor Department of Biology College of Science~/ Signature----~-----"'""""""'----- Date 3) Member (External Examiner): Ali Khalfan Al-Wahaibi Title: Assistant Professor Department of Crop Sciences Institution: Sultan Qaboos University Date 0 3· 0 ~ - .?a! j) Signatu; A4- If:_:; ~ VI This Master The i is accepted by: Dean of the College of cience: Professor Ahmed Murad 19nahrre ____-T __ __� ���-------- Date Dean of the College of Graduate Studies: Professor Nagi T. Wakim Signature Copy J- ofI Vll Abstract Ticks are \ ell known to transmit various pathogens including bacteria, viruses and protozoa to humans and animals. The soft tick (Omithodoro mllesebecld) was common on a breeding colon of the Socotra co mloran t (Phalacrocorax Jligrogu/ari ) in iniya Island, the United Arab Emi rates (UAE). The aims of the stud were: i) in estigating the prevalence and conduct genetic characterization of the inlportant bacterial pathogens Borrelia spp. (causal agents of relapsing fe er), Rickettsia spp. (cau aJ agents of spotted fe er), and Coxiella burnetii (causal agent of Q fe ver); ii) understanding the overall bacterial community associated with 0. 11111e ebecld by using Illwnina-based metagenomic approach; and iii) establishing a molecular record of 0. mZle ebecld based on mo lecular markers. Ticks were collected from the largest breeding colony of Socotra Cormorant in 2013 and 20 16. Subsequently, genomic D A was extracted from each tick, and conventional PCR assays were used to detect certain pathogens. Borrelia spp. and Rickettsia spp., were not detected. Howe er, PCR assay and metagenomic analysis indicated the presence of the Coxiella genus. Sequencing results revealed 809 bacterial operational taxonomic units (OTUs) within the five samples from 2013 and 2686 OTUs within the 5 samples from 2016. Metagenomic analysis showed that Firmiclltes, Proleobacteria, and Bacteroidete are the most dominant phyla. C. bumetit was the most prevalent species in all samples in 2013 and 2016. This data provides the complete picture to date of the bacterial communities present within 0. muesebecki under natural conditions in the UAE using high-throughput sequencing technologies. In addition, this study provided the first DNA mo lecular record of O. mZle ebecki in GenBank. Further investigations regarding the functional role of Coxiella in seabird colonies is needed. Keywords: Metagenomics; Socotra cormorant; Ornithodoros muesebecki; Coxiella bU771etii Bacterial community diversity; Next-generation sequencing; Illurnina. Vlll Title and Abstract (in Arabic) tj�1 lJ:.li1 JI�l:�.;-JI �� I wI.,,�') all ���I �I �� wl..)14'i1�J J c) (,$�I yLbll O.)A.;j,'U � (Ornithodoros muesebeckl) o�I��1 �I . ." 'luU)IJ l \......u .. �'1 L . � I�L:, <GL _. <'I u. �::..A_iliib.l' -' u -'� -' _ � I � <Y='.JA1 'Jrl G�.. (J:l . �I ?.::1 1 (.......Sy...: yUJ\ � � �I-, 0� � (0. l17ue ebecki) t �)UI �I �\yJI � .ul�l-, o� w� .o�1 �y...l\ G\.JL.),\ 4J-,� � 0;jJI r' o.JL.\ � � oJ:l..? � l,?�\ . '.J I � L ':<.11 �x � .L'tl <Y='. \ �.. I _ �. c...)A Glc.� .J� \ � �. I (1) c.S'I -' .J-<=> J .J �I)I �\ �yJ �\ (Borrelia spp.) �fo. � �� �ji-, �I (Coxiel1a burnetii) �fo.-, �\ �\ �yJ �\ (Rickett ;a spp.) 2ll�-, �\yJ\ � �yJ\ 4�1 G� 4jtS � wy.J.lI (2) �Q � � �yJ \ L.»U �\.;.u\ � �jlll .J� -' ���� �\�� 0A . t�)U I �\ (3) I �I A)\O'; 2013 (.,?"lc. � l,?�\ ylblJ ° � ySi 0A �\yJ\ G� � ti '�\.J�\ o� J� l,?j��\ Jc,u:J\ r\�� � JS 0A l,?-'yJ\ �\ <Y='�\ � ,� lJ-a-' .2016-, � lJ-a �fo. l,?i uc �\ M rI . ��\ ��\ uc � peR J'I!I..;jJ\ lY> �fo. �y:...J �l G)... .:u l ���\.J (,,7\...\";;\\ �\ �lij USJ d_�• .•� )\-, 41::.J�\ � 4..;fo. 4),;/"",,) O.l.:o..-, 809 �y:..-, uc ("7\...\...),, �\ �lij �-' . �fll t..Ji rlc. lJ-a u� �\ � 4..;fo. 4/')''' ''''' O.l.:o..-, 2686-, 2013 rlc. lJ-a G� �\ ,Firrnicutes 4..;�\ Glc.�\ ui ���\ �\ �l-, .2016 �fl\ �fo. ul.J .I.J�\ �\ ysl G..itS Bacteroidetes-, Proteobacteria ut..jl��1 o� .2016.J 2013 (.,?"lc. � u�1 � � I.J�\ t..Ji ysl G..itS �.Jy' W=...:i O. mue ebecki�\.J � o�y:..�\ 4..;�\ ul, AI? JJ u')\ � o.J� L5�1 G.,;9-, 4j�)'� .(Llj�1 �lc. (,,7\...\...)\\ � GI)"o'; �\�� G\.JL.),I 4J-,� �\ w.J.;b11 � � O. mue. ebeck �\yJ l,?-,yJI ��..? � J) �\.J�\ o� G...,� ,2lJ� �l u� LSy...i u\......u\.J� �\..?)' o.J-'� �� '�\J�I o� � �� .Genebank G�\ .4..;�\ .J�\ G\� � �fll �� �)\ .J.J�\ yUJ\ ��\.JA)U �\ t�)U\L.»U\ �\yJ\ ����\ �I :�yl �\ �liA .�)J �(,,7\,,!\"',1I �\ lJ-a ��W\ Ji..:JI �l,?�1 �\ t.iU �l,?�\ lX Acknowledgements I v ould fir t like to thank both Dr. Mohammad I-Deeb and Dr. Sabir bin Muzaffur fo r their help and guidance. I \ ould also like to thank Dr. Mohammad Taber, Dr. Gaber Ramadan, Dr. Mohammad Anan and Ms Raja Al Muskari wbo assisted me " ith my laboratory work. I am grateful fo r your help and support. My sincere thanks extended to Ahmed Taha (Library Research Desk) fo r his thorough work of editing and proofreading. I appreciate my wonderful fa mily fo r their constant encouragement and support, in particular, my mother, Azza aif AlKayoumi. She is tbe greatest mom, an extremely good listener and a good thinker too. Whenever I fe el I would like to talk to someone, she is the one who immediately comes to my mind. She always cultivates positi e thoughts in my mind, and I never start my day without ber prayers. She taught me that I should keep on learning and make some mistakes in this life because as she says, 'you won't learn if you ha en't made mistakes in your life'. I would like to associate myself with Jubran Khalil Gibran, the Lebanese scholar, who said that 'The three most beautifZlI women in the world: my mother, her shadow, and her reflection'. I totally agree with him that you are a truly beautifulwoman on the inside and out. May Allah bless you and protect you. I would like to thank my friends andcol leagues. Their contagious energy motivated me every single day. Their precious words were the fuel which enabled me to accomplish my project. I will never fo rget their empathy toward me when I fe lt down. They strengthened me and took out the pain inside my soul. Thank YOll! IX Acknowledgements I would first like to thank both Dr.